The emergency unit at the Marsa abattoir was closed off and disinfected after rats were found during a routine inspection two days ago.
All the meat from animals slaughtered at the abattoir was destroyed immediately, a Resources Ministry spokesman said.
Evidence of the rodents' presence was found in the abattoir's emergency area on Thursday. The section is used to put down injured horses or goats that would have broken their legs, for example.
The authorities are suspecting the rats got into the abattoir by gnawing away at the rubber that seals the doors or through the drains.
There was no cause for alarm and no danger to food safety, the spokesman said. "All the meat in the section was destroyed and the area was thoroughly disinfested," he added.
During an inspection on Thursday, "some shortcomings" were noted and immediate action was taken to rectify them, the Veterinary Services Division said.
"There are no grounds for alarm, controls are meant to ensure public safety at all times because of the nature of the place," the division said. The reported shortcomings were limited to the emergency section only and not the whole abattoir.
It added that, in the immediate future, the emergency section would be closed and the slaughter of horses, goats and sheep would take place in the abattoir.
Last November, puddles of blood had formed outside the abattoir and the roads of Marsa. According to the ministry and the Water Services Corporation, they were caused by illegal dumping in the sewers.